[BiO BB] command-line (scriptable) ORF finders?

Ann Loraine aloraine at gmail.com
Mon Sep 18 11:05:18 EDT 2006

Thank you very much for the pointers...it was very helpful.



On 9/18/06, Stefan Rensing <stefan.rensing at biologie.uni-freiburg.de> wrote:
> Hi,
> > (1) I am looking for a command-line, scriptable tool that can take as
> > input an EST, cDNA, or assembled EST contig ("unigene") sequence and
> > return the most likely or longest open reading frame. This is for a
> > plant EST project.  It should also pay attention to codon usage rules.
> We found FrameD to be superior to ESTScan and Estwise in predicting ORFs
> in moss (P. patens). We are using species-specific (i)HMMs, repectively.
> http://bioinfo.genopole-toulouse.prd.fr/apps/FrameD/FD
> http://bioinfo.genopole-toulouse.prd.fr/apps/FrameD/Help/FrameDWeb_5.html
> > (2) I am also looking for a tool that can take as input a set of exon
> > annotations (or mRNA-to-genome alignments) and return the most likely
> > CDS start and end for the given gene structure. Tools that can jigger
> > the alignment/exon boundaries to optimize the ORF *and* which pay
> > attention to codon usage rules would be extra great. This is for
> > deducing novel gene structures from cross-species mRNA-to-genome
> > alignments. Maybe there is a gene-finder that does this?
> You might want to have a look at GenomeThreader,
> http://www.genomethreader.org/, which allows spliced alignments using
> non-identical mRNA/protein sequences (i.e., homologs from other species).
> Cheers, Stefan
> --
> Dr. Stefan Rensing, Group Leader Computational Biology
> Plant Biotechnology, Faculty of Biology, University of Freiburg
> Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945
> http://www.plant-biotech.net/  http://www.cosmoss.org/
> stefan.rensing at biologie.uni-freiburg.de
> "There is science, logic, reason;
>  there is thought verified by experience.
>  And then there is California."
>                                           Edward Abbey
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Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham

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